Some (not all) are shared.
Some I own but have links to another directory.
Some I own and created, but the most recent update was done by some else I shared the file with.
Some I cannot figure out any difference at all. (I.e. I own them, they exist only in one folder, and I am pretty sure have only been updated by me.

Please wait until the release of the next version of FileZilla Pro. Once you have updated to the next version, connect to Google Drive. Next enable "Show raw directory listings" on the debug page in the settings and refresh the directory listing. Copy the raw listing from the message log and past it here. Give an example of some of the file visible in the raw listing that aren't displayed in the remote file view.

As I am downloading more than 30,000 file across more than 1,000 directories, I wish there was some sort of auto-truncate option (or remove vowels except for leading ones) from file names and optionally, directories.

There are also files that Google does not show because they are shared with me. I have full access manually downloading them using the web interface, but using FileZilla.